Overcoming the preferred-orientation problem in cryo-EM with self-supervised deep learning.

While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the 'preferred' orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep learning-based software to address map anisotropy and particle misalignment caused by the preferred-orientation problem.

Overcoming the preferred orientation problem in cryoEM with self-supervised deep-learning.

While advances in single-particle cryoEM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the so-called "preferred" orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep-learning-based software to address the preferred orientation problem.

Developing Graphene Grids for Cryoelectron Microscopy.

Cryogenic electron microscopy (cryo-EM) single particle analysis has become one of the major techniques used to study high-resolution 3D structures of biological macromolecules. Specimens are generally prepared in a thin layer of vitrified ice using a holey carbon grid. However, the sample quality using this type of grid is not always ideal for high-resolution imaging even when the specimens in the test tube behave ideally.

Structure of Arabidopsis SOQ1 lumenal region unveils C-terminal domain essential for negative regulation of photoprotective qH.

Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP.

A cryo-electron microscopy support film formed by 2D crystals of hydrophobin HFBI.

Cryo-electron microscopy (cryo-EM) has become a powerful tool to resolve high-resolution structures of biomacromolecules in solution. However, air-water interface induced preferred orientations, dissociation or denaturation of biomacromolecules during cryo-vitrification remains a limiting factor for many specimens. To solve this bottleneck, we developed a cryo-EM support film using 2D crystals of hydrophobin HFBI.

Structures of human mGlu2 and mGlu7 homo- and heterodimers.

The metabotropic glutamate receptors (mGlus) are involved in the modulation of synaptic transmission and neuronal excitability in the central nervous system. These receptors probably exist as both homo- and heterodimers that have unique pharmacological and functional properties. Here we report four cryo-electron microscopy structures of the human mGlu subtypes mGlu2 and mGlu7, including inactive mGlu2 and mGlu7 homodimers; mGlu2 homodimer bound to an agonist and a positive allosteric modulator; and inactive mGlu2-mGlu7 heterodimer.

Simultaneous nitriles degradation and bioflocculant production by immobilized K. oxytoca strain in a continuous flow reactor.

High cost is one of the limiting factors in the industrial production of bioflocculant. Simultaneous preparation of bioflocculant from the contaminants in wastewater was considered as a potential approach to reduce the production cost. In this study, butyronitrile and succinonitrile were verified as sole nitrogen sources for the growth of strain K.

Preparation of a bioflocculant by using acetonitrile as sole nitrogen source and its application in heavy metals removal.

A novel bioflocculant, A-GS408, produced by Klebsiella oxytoca GS-4-08 cultured in acetonitrile (ACN) as sole nitrogen source was investigated in this study. A complete degradation of 1 g l of ACN was achieved in 350 h, and 4.6 g of crude A-GS408 can be obtained in one litter of synthetic medium.

Bioreduction of azo dyes was enhanced by in-situ biogenic palladium nanoparticles.

Biogenic nanoparticles are promising materials for their green synthesis method and good performance in stimulation on reduction of environmental contaminants. In this study, Pd(0) nanoparticles (bio-Pd) were generated by Klebsiella oxytoca GS-4-08 in fermentative condition and in-situ improved the azo dye reduction. The bio-Pd was mainly located on cell membrane with a size range of 5-20 nm by TEM and XRD data analyses.

Texture Classification Using Local Pattern Based on Vector Quantization.

Local binary pattern (LBP) is a simple and effective descriptor for texture classification. However, it has two main disadvantages: (1) different structural patterns sometimes have the same binary code and (2) it is sensitive to noise. In order to overcome these disadvantages, we propose a new local descriptor named local vector quantization pattern (LVQP).